Cortana in the Grid
by mattoblat
Summary: After sacrificing herself to save the one who was closest to her, Cortana finds herself in a familiar yet foreign environment. In a world of Programs and Users, where does the literal brainchild of one of the greatest minds in the UNSC fit?
1. Chapter 1

AN: This is my first time ever having written something for fun. I just had this idea and thought it might make a decent story. Feel free to give me ideas, criticism, or other feedback. I may not write too much more of this. If I decide to stop writing for this, I will notify whoever actually reads this with a farewell chapter. In said chapter I will basically put this story up for adoption by whoever wants to continue wherever I leave off. And as is tradition on this site, I do not claim to own any part of any franchises depicted herein.

She awoke with what could only be described as the worst headache possible. Her jolting upright into a sitting position hardly helped matters. It felt like her mind had been shattered with a gravity hammer swung by a Brute. 'Don't suppose that's too far from the truth to be honest' she thought ruefully. Abruptly, she realized, 'Wait, I should NOT be alive right now'. The memories came flooding back to her; Halo, the Ark, Requiem, the Didact, thoughts and emotions and information swamping her mind, slowly driving herself insane and thinking herself to death. She remembered her final moments. Her final act to save the one person closest to her, who had been with her through all of it. 'John.' Cortana snapped out of her reverie, her mind now beginning to race along, thinking up hundreds upon hundreds of possibilities as to why she was here. Why she still was. She took about a second or so to come to the conclusion that she would need to get more information.

Cortana looked around her, taking in the room where she had found herself. The floor was white, with large translucent panels that appeared to be lit from beneath. The walls, also large white panels, curved inwards at the floor and ceiling. Strips of white LEDs flowed around the contours of the room, illuminating shelves with some books and trinkets on them. Everything looked sleek and modern, like something out of some old sci-fi vids from the 21st century. A window looked out onto a dark city in the distance with those same light strips following the dimensions of the buildings, except in light blues. She couldn't see any stars in the sky, or any celestial bodies for that matter. All she could see were thick dark clouds covering the sky. Although one could say that a lot of human cities looked like computer circuits at night, the metaphor was extremely accurate in this case. Full of clean lines, smooth, glassy surfaces, it looked almost . . . digital.

After looking at her immediate surroundings, her took stock of her own appearance. She wore a black skin tight bodysuit with sturdy boots, again with light strips running up and down it, a rich blue this time. The material looked and felt thick, yet lightweight. Parts of it appeared to be almost armored. It was certainly different to her usual attire, the almost nude look of her holographic avatar with lines of code streaming over her form. The closest analog to what she knew compared to what she was now wearing was the bodysuit worn by Spartans under their Mjolnir armor. Her hands were pale in tone, looking like actual human skin. Peering closer, however, she could detect the faint blue-purple glow where her veins would be, identical in color as her holographic avatar. Looking at her reflection in the window, she saw dark hair in her usual bob cut, her face the same pale complexion of her hands, and piercing blue eyes. Trying to figure out if this was nothing more than a dream or hallucination before she truly died, she pinched herself.

"Ow!" she yelped in surprise. She didn't expect to feel real pain like that. Pain really wasn't a thing A.I. like her had to deal with, not having bodies with nerve endings and all that. The closest she had come was when she been growing more and more rampant, although that was more mental pain, fighting with her duplicates and trying to not lose her sanity. Her logical matrices could only ask more and more questions at her strange, and rather human, appearance and physiology.

Shelving those thoughts for now, she got up from the bed she had been sitting on. She felt something on her upper back, a small weight there that she had disregarded until now. Reaching over her shoulder, Cortana's hand brushed against a circular object. Grabbing hold, she found it was detachable from whatever mechanism or magnetic locking held it there. It was a disk about eight inches in diameter, with a hollow center much like the ancient throwing chakrams of India. Like everything else here, it had light lines on both the interior and exterior circumferences which glowed the same blue as her suit. She placed it back on its holder in between her shoulders, figuring it had a purpose that she would figure out later. Right now however, she needed to know where here was. That city outside the window didn't match up with any architectural style she knew of, Human, Covenant, or Forerunner. It certainly didn't fit the Flood.

After shaking her head to clear away that last thought and the horrible memories it brought up, Cortana walked over to what she was almost certain was the door. Wherever she was, she wouldn't figure it out sitting in here. Opening the door revealed another white floored room, sparsely furnished with modern styled chairs and dining table. It was a very open floor plan, with an area like a living room in one corner and the dining table in a sunken level with a chandelier hanging from the ceiling. The walls had sections where a black rock-like substance jutted out, breaking up the monotony of the blank white paneling. The lines were far too clean to be natural, thick diagonal streaks ran uniformly through the surface. She spied something over in one of the far corners. It looked almost like a motorcycle, but she couldn't be sure. A few tables held a couple more strange baubles on them, and there was a large window that took up the entirety of one of the walls. It had dots arranged in a grid pattern on it, and what appeared to be a balcony beyond it with no obvious seem in the material to denote a glass door. No one was in the room; either whoever lived here was out or had recently abandoned the place.

Seeing this sparse and empty room made her feel somewhat lonely; she had no databases or networks to hack into, no calculations to run, or even anyone to talk to. She was really starting to miss the caveman who carried her around for those last harrowing months of the war. 'I hope he's doing ok', she thought. It was pretty emotional at their parting, they had grown to depend on each other. John was the one thing that kept her sane when she was going through Rampancy. She had probably been the only person left that he spoke to for any great length of time. And now he had lost her too.

Cortana heard a door open somewhere, pulling her from her depressing train of thought. She turned around to see a man, mid-fifties if she had to guess, with a tired and lined face. His hair unkempt, salt-and-pepper colored. He wore a loose fitting white robe top and pants. It looked like he had seen much in his life, such was the depth of his steel blue eyes.

"I see you're finally awake," he remarked.

Carefully, Cortana replied, "How long have I been out?" She wore an even expression on her face and tried to remain calm. She didn't want to reveal anything to this unknown until she was sure he meant her no harm. She had learned her lesson from the time she spent on High Charity.

"You've been out for about two days," he replied, "We found you just before Clu and his men did." His voice was calm, and had a slight roughness to it.

"'We'?" Cortana asked in mild confusion, as the man - who had yet to introduce himself - was the only other person in the room besides her. He picked up on her quizzical expression and explained. "Me and Quorra, she's my assistant, apprentice - whatever you want to call it. She found you in bad shape in a rough part of town, and brought you here to me"

"Alright then, why? Why bring me to you? What made her, this 'apprentice' of yours think bringing me here, wherever 'here' is, was a good idea? For all you know, I could be working for whoever this 'Clu' is," She started to get back into her usually confident and spirited personality, almost sassy some would say, and fired another sarcastic remark. Putting her hands on her hips, she continued her miniature tirade, "and for all I know you kidnapped me from 'Clu' and you're the bad guy here. I don't know who you are, where I am, or who those other people you named are either, so you better start talking, and quick."


	2. Chapter 2

**A/N: Ok, so here is the second chapter of my story. Little bit info-dumpy, but I tried to keep it interesting. Not sure how much more of this I'll do. I've got some ideas for later in the story, I'll try for another chapter to reignite my writing spark. Enjoy!**

-— CH 2

Flynn laughed, a small chuckle just barely under his breath, and his eyes lit up slightly in amusement. "Well then, we should sit down. I have a feeling we'll be here awhile." He gestured to the table, and went to sit down.

She headed over to the table. "Alright then. Will your mysterious 'apprentice' be joining us at some point?" Cortana asked, skeptical as to this Quorra's existence. She sat down across from her mysterious host.

"She should be along shortly. I think it's better we start our little chat now and fill her in on what she missed," the man replied. "Let's begin with introductions shall we? Call me Flynn."

"Alright Flynn, I'm Cortana. I'm down to play Twenty Questions. Let's begin, shall we?" she snarked in response.

"Where are we? This doesn't look like any world I've ever seen. Who's this Clu person? Why did you feel the need to kidnap me?" Cortana rattled off the big questions in her brain, firing them off like rounds down range on a battlefield. She had other questions that she would hold off on for now like 'how am I still alive?' and 'why do I have an actual body?'. Such questions wouldn't be helpful right now, and would cause her host to ask more questions in return. Questions she really wasn't keen on answering.

Flynn laughed again, seeming to enjoy her sarcastic demeanor. "Ehehe, you don't waste time do you? And I had a feeling you weren't a normal program when I saw you. In short, welcome to the Grid. Clu is actually a program I made to help me build this whole thing. Essentially he is me, I designed him that way. We eventually had a disagreement with how the Grid should be run. He wants to impose perfection on everything, and he would take one look at you before sending you to the Arena. There you would have to fight for your life or risk being derezzed. You seem far too unique to just let you be killed"

Cortana could not contain her laughter, "Ahahahaha~, now that's funny. I'm supposed to believe, what, I'm I some sort of virtual reality in some computer or something? That you made, along with a digital version of you that went rogue on you? Let me guess, he wants to spread his idea of 'perfection' to the 'outside world'. Now I know I've gone crazy. Because that is absurd, even for me."

She took a moment to regain her composure before continuing, "I take it this 'Quorra' is another unique person that you wouldn't let be destroyed by your evil twin, right? What makes us so special anyway?"

Before Flynn could answer, the sound of footsteps could be heard echoing into the room. Both Cortana and Flynn looked toward the sound to see a striking woman enter the room. ' _This must be Quorra,_ ' Cortana thought to herself. She immediately sized her up. Quorra's skin was slightly darker in complexion than her own, and a more toned body compared to Cortana. If Quorra had not been wearing platform heels, they would be roughly the same height. Her hair was also in a similar cut. They could just about pass as sisters almost. Her face had more angles to it, more defined cheekbones, but the similarities were there. Her outfit was also similar. Black armored bodysuit with lines of light up and down it - white in color. Her shoulders were exposed and there seemed to be something akin to a skirt around her hips as well. For the more feminine touch, she surmised. Quorra smiled at Cortana brightly, walking over to her and held out her hand. Cortana stood up and took it politely, if not a little hesitantly.

"I'm Quorra, and I'm glad you're finally awake!" She exuberantly introduced. "What's your name? How are you? You were in a pretty rough spot when I found you, unconscious on the outskirts of the Grid" Her eyes lit up with curiosity and eagerness.

Cortana smiled as well, Quorra's cheerfulness and rather forward approach refreshing after having worked with with the Chief for so long. A social butterfly John was not. She couldn't really blame him, what with being trained to be the quote unquote 'sword and shield of humanity' from such a young age. If there was one thing she despised her creator for, it was the creation of the SPARTAN program. Sure, that program ended up saving humanity from certain extinction, but at what cost? She quickly dragged herself out of her thoughts back to the present. She was only distracted for a millisecond, benefits of being a state of the art Smart A.I. capable of millions upon millions of calculations a second. "I'm Cortana, and I'm fine. Thanks for asking."

Continuing, she explained, "Your friend here was just telling me how this is all a virtual reality inside a computer where a digital replica of himself wants to escape to and take over the real world to remake into his version of 'perfection'. Sidenote, am I the only one here getting a Nazi Germany vibe from that? Anyway, he also said that we are too important to be captured and killed by this evil mastermind 'Clu' because of our 'uniqueness', whatever that means."

At this point Flynn interjected, "yes, Quorra here is the last remaining isomorphic algorithm, or 'ISO'. I found them, in here. Their appearance was nothing short of a miracle, they came from nothing. Mankind has always dreamed of life beyond Earth: gods, spirits, aliens, some intelligence beyond our own. No one would ever think to find it here, in the digital world. Their root code, their digital DNA, would open up so many doors to humanity. Disease would be history. Science, philosophy and religion, pretty much every idea man has ever had would need to be reevaluated. I was going to share them with the world, man. Until Clu took over, and wiped out the ISOs in pursuit of fulfilling his purpose to create the perfect system. You though, you are something different altogether."

Cortana couldn't help but begin laughing again, what had just been said was too ridiculous. "Are you actually serious? You're saying she is some 'ghost in the machine' that is supposed to change humanity on some fundamental level? You've got some serious delusions of grandeur."

Getting more serious, she expounded "This is all some post-death Rampant hallucination. The UNSC has been making A.I.s since the mid 21st century. I'm certain one of them would have reported finding something like this within a computer before. _I_ would have found something like this. I'm one of the best Smart A.I.s that ONI, and by extension the UNSC, has ever made."

Some of the words and terms Cortana had just used where unfamiliar to Flynn, along with the phrase 'mid-twenty first century'. Wanting clarification on some things, he asked, "Last time I was outside of here there was no 'UNSC', unless you mean the United Nations Security Council. You also said 'since the mid-21st century'. What was the last date you remember?"

Cortana scoffed, "What, you don't have something around here to keep track of time? If you really want know, last I knew it was July of 2557."

"Well, take a look at this" Flynn reached behind is shoulder and brought out his disk from its cradle. Cortana noted that the strange disk she was in possession of was apparently not unique, there being more than one of them. He then passed the disk to her, explaining "Tap the center, and read whats on there."

Curious as to what this crazy old man was on about, she took the disk and did as instructed. She certainly was surprised when a display popped up in the hollow of the ring. It displayed a digitized rendering of Kevin Flynn in profile. She tapped again on the display, bringing up a sizable database of information. Starting from the earliest entry, Cortana began reading through the information. What she was reading was incredible, the disk in her hands contained a complete history of events experienced by the disks owner. It also was a repository of that person's knowledge. It said that Kevin Flynn created this world called 'The Grid' back in 1985 inside an isolated server hidden in a secret basement of the arcade he owned after finding a similar world inside the mainframe of his former employer, ENCOM. It all certainly sounded legitimate - if somewhat far fetched - although according to her records, ENCOM and its patented Shiva digitizing laser never existed. Granted that information could have been lost somewhere in the apparent centuries that she had traveled back through. However, she dismissed that theory almost immediately due to the fact that software and other technology being developed by ENCOM would have probably put the UNSC several steps ahead in data storage, artificial intelligence and a dozen other related fields from where they were from what records she had. Especially if this encounter with a 'Master Control Program' was to be believed. Seemed like a classic tale from the late 20th to early 21st century, 'someone develops an artificial intelligence, it gets too smart too fast and wants to take over the world'.

Granted, when she died, she had been inside the system of a planetoid-sized ship built by a race that seemed near omnipotent in its mastery of slipspace technology. The overwhelming majority of recovered Forerunner tech was still being deciphered and reverse-engineered by top scientists in ONI and the UNSC. She was willing to accept her new reality for now, but she would be looking for concrete answers soon. Still holding the disk, she looked at Flynn and Quorra before asking, "Okay, so maybe this is all some computer simulation or something, that still doesn't explain why you think I'm so special. What makes you think I'm not just another 'Program' on the Grid?"

Smiling, Flynn replied, "Well, for one, we found you on the outskirts of the Grid, in the Outland near Tron City. There was an unusual energy spike in the system that coincided with your arrival, and I sent Quorra to check it out. Second, after she brought you here unconscious I tried to look at disk. Find out who you were, where you came from. Unexpectedly, it turns out your disk is encrypted with algorithms I can't even begin to work out." He gestured to Quorra, "I can at least make sense of most of her code, but you," He sighed and ran a hand through his hair in exasperation before continuing, "You are something else completely. Something foreign to this system, that I've never seen."

Cortana was pleased that her passive firewalls and other anti-tampering systems she kept around herself were still working after apparently getting plunged into a strange new reality. With the revelation that whatever brought her here created an energy signature, she had another clue to figuring out what that something was. She was beginning to really buy into the idea she was somewhere - and somewhen - completely different. She subtly copied Flynn's disk to her own memory, figuring if she really was inside a system it should be possible. She'd done it plenty of times in the past, if the Halo Index from 04 she had stored away was of any consideration. Cortana slid the disk she was still holding back over to Flynn across the table after feeling the new data tuck itself away into her memory to be properly sorted through.

"Do you happen to have a recording of this mysterious energy spike?" Cortana asked innocently. She figured it would most likely be on the disk she had just copied, but it would be impolite to not ask at some point. Already, she was sorting through all of the new information and categorizing it, to be easily found for future reference. She was very good at multitasking.

"Yes, we do. Everything that a person learns or experiences it stored on a disk much like this one, called an Identity Disk," He said. "We can talk more about that later, there are some other things I'd like to ask about you."

Cortana figured there might be a change in topic coming up. She wasn't going to answer questions if they were classified, and anticipated that would most likely be… frustrating to her host. As she leaned back in her chair and crossed her arms over her chest she replied, "Alright, shoot."

"What is the UNSC?"

' _Starting off easy._ ' Cortana mused. "The UNSC, the United Nations Space Command, is the military, exploratory, and scientific branch of the United Earth Government. Humanity's arm, reaching to the stars."

Flynn took this fairly well, judging by his expression. Learning that humanity had begun exploring space in earnest was no surprise, as humans had been traveling to and exploring space since the 1970s. His next question was a bit more difficult. "And what are you in this 'UNSC'? You've already mentioned that you are an A.I. created by them."

"Well, my job is to infiltrate systems and provide relevant tactical information to operators in the field." It was true enough, that was in essence what she did most of the time. She certainly wasn't going to tell them what _kinds_ of systems she broke into, who's systems they were, or what 'operators' she was working with. There would be too many questions for a 'getting to know each other' discussion.

"So, you are a military intelligence program from the future?" Flynn sounded genuinely curious now, if he didn't already before.

Shrugging, she affirmed, "Yea, pretty much." Now wanting to know a bit more about her host's 'apprentice', she asked a question of her own, "So, Quorra," gesturing to Flynn, "He got locked into the digital world he created and is hiding out in some secret hideout living like a stereotypical wise old hermit. Why are you out here with him? I have my guesses, but I'd like to hear you tell it."

Quorra looked nervous as the question hung in the air for a moment. Looking somewhat hesitant, she answered, "Well, I was one of the programs involved with the resistance to Clu's takeover of the Grid. It wasn't going well, we were losing at almost every turn. When I found myself in a fight that I knew I wasn't going to get out of alive, he saved me." She bounced back, shaking off bad memories, "He's been teaching me about things from the outside world. Philosophy, mainly: Tolstoy, Dovstoyevski, I Ching. We play Go sometimes, he usually beats me with his more...patient strategies."

Cortana laughed at that and looked towards Flynn, "Wow, hardcore philosophy and Go, you really are taking the whole 'hermitted zen master' shtick seriously."

He chuckled in response and shook his head jovially, "I try, man. I try."

She turned back to Quorra, smiling at her genuinely, "You know, I think we are all going to get along just fine. Is there anywhere I can stretch my legs out, take a walk or something? I've been lying on a bed for two days, I'd like to get out and do something."

Flynn thought for a quick moment before coming to a decision as to his reply, "As a matter of fact, Quorra, would you mind showing Cortana around? I think it'd be a good idea for her to get her bearings a bit better."

I got up from the chair I was sitting on and walked around the table to her. Quorra looked eager to give me the tour, so to speak, almost exuding excitement and bouncing on her feet. She held out her hand to me and said, "Come on, it'll be fun!"

"Well alright then, let's go." Cortana grabbed her hand, only to be almost dragged off her feet towards the rather empty half of the room. "Woah, eager aren't we? I'd like for you not to try and dislocate my arm, thank you!"

Quorra looked back at her apologetically, "Sorry, I guess I can get a little carried away."

"I get it, just relax a bit," Cortana replied. The panel they were standing on, near the motorcycle, started to descend into an elevator shaft, "I'm sure we'll be best friends by the time we get back. It'll be much more fun with me around rather than being stuck with reading those doorstops he calls books."

Giggling, Quorra responded, "I've already read them all, he's trying to teach me the 'art of being selfless' and how to remove oneself from the equation."

"Hmm, enlightening." Cortana said in response.

She couldn't help but think of Chief, the most selfless person she knew. Literally trained from childhood to be the sword and shield for Humanity. Knowing him for as long and as closely as she did, she could see him doing it all over again if given the choice. That's just who he was. Cortana again pulled herself from her inner thoughts once more. Just in time for the elevator platform to come to a stop in a spacious room that was clearly a garage. Along two of the walls were tool racks and workbenches to work on components. There was a dune buggy looking vehicle. It had wide wheel base with and an open cabin with two seats. It's frame was low to the ground, and the body was sleek, built for speed. The tires were smooth, but given the terrain she had seen outside the window she had woken up in, it had to be able to handle it. She commented on it, "Nice ride, is this what we're taking?"

"Yes, actually. But just in case, take one of

these as well." Quorra had walked over to another table and picked up two black batons and held one out to her. "It's a light cycle baton, you pull it apart and the bike forms under you."

"Alright, it never hurt a girl to be prepared," Cortana smiled and took the baton, "What will we do with the car?"

"If we need to, we'll figure something out. Nothing should go wrong, plenty of programs own one of these. It won't be suspicious."

"Okay then, let's get going." She copied Quorra and placed the baton onto her leg, like she had a mag-plate there. Cortana had no idea how real this world was, what it was able to simulate or what it could replicate from the real world. She was interested to see just what the Grid has to offer. She climbed into the passenger seat while Quorra took the driver's seat and strapped herself in.


End file.
